I am not a native speaker of English. I came across many articles which used the phrase "pun intended". In many cases I am not able to grasp the meaning of the sentence as what this phrase mean in the context. For example,

Behavioural experts say it is not just the wiring that causes the ‘differences’ (pun intended).

I am totally clueless about what the meaning of the phrase inside the braces is. What does it mean?

Can you give some previous sentences to give more context? It's hard to tell what pun/double meaning is being referred to, intended or not.
– MitchJun 30 '11 at 14:00

2

@Mitch: It's probably electrical. Electrical voltage is more properly referred to as "potential difference" across a circuit. In certain work/study environments it's often shortened as "difference" instead of voltage. From the snippet, I would assume that the article is about behavioral anomalies caused by voltage fluctuations or variances in certain parts of the brain.
– TobyJun 30 '11 at 15:51

@Mitch its in some article about behavioral differences between men and women. "wiring" here has references to brain neural connections
– bubbleJun 30 '11 at 16:31

Well, it could be a very poor pun. Or the writer is using the word pun inappropriately.
– MitchJun 30 '11 at 16:42

@Mitch I also have the same feeling that the writer is using it inappropriately.
– bubbleJul 8 '11 at 10:26

I'm surprised that nobody has mentioned that the phrase "pun intended" is a form of wordplay itself:

As others have commented, a pun is a play on words, usually using words that sound the same or similar to give multiple meanings to a phrase.

Sometimes when writing or speaking it is hard or unavoidable to use a phrase that creates such a double meaning - potentially obscuring the speaker's point and/or making it seem like they are joking. In this situation it is common for people to say

(No pun intended)

This, I believe, is the original phrase.

Playing on this, some people occasionally reverse the phrase by removing the negative:

pun intended

to make it clear to the listener that yes, they are using wordplay to make their point.

(Interestingly Google has ~11 million hits for "pun intended", but ~21 million for no pun intended, even though every page that contains "no pun intended" must contain "pun intended"!)

"Pun intended" literally means "There is a pun (a play on words) in this sentence, and I put it in intentionally." This distinguishes it from unintentional puns, where the writer didn't mean to put it whatever double-meaning is there.

Unfortunately the example sentence you give doesn't have enough context for us to tell what the pun is; I would guess that either "wiring" or "differences" is used in a slightly different way in the previous sentences.

The pun, also called paronomasia, is a form of word play which suggests two or more meanings, by exploiting multiple meanings of words, or of similar-sounding words, for an intended humorous or rhetorical effect.

Pun intended probably is used to indicate that the ambiguous phrase was intentional.

Of course, as many have explained, "pun intended" means that the pun is deliberate: can't argue with that!
However I think that in many cases the author slyly draws our attention to the fact that there is a pun, which might otherwise have escaped us readers.
Anyway, it often happens to me that I only notice a pun because of this kind of remark, in English of course, but even in my native language, French.

Thank you for your interest in this question.
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